CNVPaneOfNormal

Call CNV from panel of normal computed with 'basecoverage'

Usage

Usage: java -jar dist/cnvpanelofnormal.jar  [options] Files
Usage: cnvpanelofnormal [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    --canvas
      Canvas output
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -f, --iqr
      IQR factor to detect outliers
      Default: 1.5
    --mapq
       min mapping quality.
      Default: 1
  * -V, --vcf, --normal
      Vcf panel of normal generated by 'basecoverage'
    -o, --out
      Output file. Optional . Default: stdout
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --runmed
       moving median size
      Default: 31
    -t, --treshold
      CNV treshold DEL if depth < 1.0 - x and DUP  if depth > 1.0 + x
      Default: 0.4
    --version
      print version and exit
    -S
      merge CNV within distance of 'x'.
      Default: 0
    -m
      min CNV size
      Default: 0

Keywords

• depth
• bam
• sam
• coverage
• vcf
• cnv
• sv

Compilation

Requirements / Dependencies

• java compiler SDK 17. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone --recurse-submodules "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew cnvpanelofnormal

The java jar file will be installed in the dist directory.

Creation Date

20241123

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/basecoverage/CNVPaneOfNormal.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite cnvpanelofnormal ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030